From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Tue Apr 19 2016 - 14:59:01 CDT

Hi all,

I am trying to solvate ferritin (it is a spherical molecule that
consists of 24 identical chains, 66456 atoms ) in a water box and keep
getting the same error regardless of whether I run it in a tcl/tk
console or graphic interface. The error is only for the first 9
residues of the first chain, total of 151 atoms. When I run solvate,
i.e.

package require solvate
solvate ferritin.psf ferritin.pdb -t 5 -o solvated

I see warnings such as these:

psfgen) no residue 1 of segment A
psfgen) Warning: failed to set coordinate for atom N THR:1 A
psfgen) no residue 1 of segment A
psfgen) Warning: failed to set coordinate for atom HN THR:1 A
psfgen) no residue 1 of segment A
psfgen) Warning: failed to set coordinate for atom CA THR:1 A
psfgen) no residue 1 of segment A
psfgen) Warning: failed to set coordinate for atom HA THR:1 A
psfgen) no residue 1 of segment A
psfgen) Warning: failed to set coordinate for atom CB THR:1 A
..
..

and so on for the next 151 atoms in a ferritin.pdb file.

When the file solvated.pdb is created, the first 151 atoms have zero
coordinates:

ATOM 1 N THR A 1 0.000 0.000 0.000 -1.00 0.00 A
ATOM 2 HN THR A 1 0.000 0.000 0.000 -1.00 0.00 A
ATOM 3 CA THR A 1 0.000 0.000 0.000 -1.00 0.00 A
ATOM 4 HA THR A 1 0.000 0.000 0.000 -1.00 0.00 A
ATOM 5 CB THR A 1 0.000 0.000 0.000 -1.00 0.00 A
..
..

In the ferritin.pdb file the same atoms have coordinates and and look
normal in VMD before I solvate the structure:

ATOM 1 N THR A 1 29.972 78.277 67.795 1.00 0.00 A
ATOM 2 HN THR A 1 30.255 79.195 67.517 0.00 0.00 A
ATOM 3 CA THR A 1 30.644 77.930 69.037 1.00 0.00 A
ATOM 4 HA THR A 1 30.049 78.354 69.834 0.00 0.00 A
ATOM 5 CB THR A 1 30.648 76.421 69.061 1.00 0.00 A
..
..

I don't understand what causes this error and why only on the first 9
residues of the very first chain?

I searched the archives, but did not find a similar issue being
discussed. Initially I thought there may be non-standard atom or
residue names that do not correspond to those in the parameter files,
but all seems to be consistent, and in any case I do not see errors of
this sort for the rest of the molecules even though the chains are
identical (and so are atom and residue names). I use
top_all36_prot.rtf for topology.

I'd very much appreciate your input!

Olga